Harvest for Guam Species List Created 13 Oct 06:03

Stage: completed
Fetched: 13 Oct 06:03
Validated: 13 Oct 06:03
Deltas Created 13 Oct 06:03
Units Normalized: 13 Oct 06:09
Ancestry Built: 13 Oct 06:04
Nodes Matched: 13 Oct 06:09
Names Parsed: 13 Oct 06:04
New Models Stored: 13 Oct 06:03
Indexed: 13 Oct 06:09
Completed: 13 Oct 06:11
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 06:03:09 -0400 by logger.rb/56815
[START] [2019-10-13 06:03:09] logged process
[START] [2019-10-13 06:03:09] create_harvest_instance
[STOP] [2019-10-13 06:03:10] create_harvest_instance
[START] [2019-10-13 06:03:10] fetch_files
[STOP] [2019-10-13 06:03:10] fetch_files
[START] [2019-10-13 06:03:10] validate_each_file
[STOP] [2019-10-13 06:03:10] validate_each_file
[START] [2019-10-13 06:03:10] convert_to_csv
[CMD] [2019-10-13 06:03:10] /usr/bin/sort /app/public/converted_csv/guam_sp_list_refs_15907.csv > /app/public/converted_csv/guam_sp_list_refs_15907.csv_sorted
[CMD] [2019-10-13 06:03:10] /usr/bin/sort /app/public/converted_csv/guam_sp_list_nodes_15908.csv > /app/public/converted_csv/guam_sp_list_nodes_15908.csv_sorted
[CMD] [2019-10-13 06:03:11] /usr/bin/sort /app/public/converted_csv/guam_sp_list_occurrences_15909.csv > /app/public/converted_csv/guam_sp_list_occurrences_15909.csv_sorted
[CMD] [2019-10-13 06:03:11] /usr/bin/sort /app/public/converted_csv/guam_sp_list_measurements_15910.csv > /app/public/converted_csv/guam_sp_list_measurements_15910.csv_sorted
[STOP] [2019-10-13 06:03:11] convert_to_csv
[START] [2019-10-13 06:03:11] calculate_delta
[CMD] [2019-10-13 06:03:11] echo "0a" > /app/public/diff/guam_sp_list_refs_15907.diff
[CMD] [2019-10-13 06:03:11] tail -n +1 /app/public/converted_csv/guam_sp_list_refs_15907.csv >> /app/public/diff/guam_sp_list_refs_15907.diff
[CMD] [2019-10-13 06:03:11] echo "." >> /app/public/diff/guam_sp_list_refs_15907.diff
[CMD] [2019-10-13 06:03:11] echo "0a" > /app/public/diff/guam_sp_list_nodes_15908.diff
[CMD] [2019-10-13 06:03:11] tail -n +1 /app/public/converted_csv/guam_sp_list_nodes_15908.csv >> /app/public/diff/guam_sp_list_nodes_15908.diff
[CMD] [2019-10-13 06:03:11] echo "." >> /app/public/diff/guam_sp_list_nodes_15908.diff
[CMD] [2019-10-13 06:03:11] echo "0a" > /app/public/diff/guam_sp_list_occurrences_15909.diff
[CMD] [2019-10-13 06:03:11] tail -n +1 /app/public/converted_csv/guam_sp_list_occurrences_15909.csv >> /app/public/diff/guam_sp_list_occurrences_15909.diff
[CMD] [2019-10-13 06:03:11] echo "." >> /app/public/diff/guam_sp_list_occurrences_15909.diff
[CMD] [2019-10-13 06:03:12] echo "0a" > /app/public/diff/guam_sp_list_measurements_15910.diff
[CMD] [2019-10-13 06:03:12] tail -n +1 /app/public/converted_csv/guam_sp_list_measurements_15910.csv >> /app/public/diff/guam_sp_list_measurements_15910.diff
[CMD] [2019-10-13 06:03:12] echo "." >> /app/public/diff/guam_sp_list_measurements_15910.diff
[STOP] [2019-10-13 06:03:12] calculate_delta
[START] [2019-10-13 06:03:12] parse_diff_and_store
[INFO] [2019-10-13 06:03:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 06:03:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 06:03:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 06:03:15] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 06:03:31] Storing 2 References
[INFO] [2019-10-13 06:03:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 06:03:31] Average Time: 0.0
[INFO] [2019-10-13 06:03:31] Total Time: 1s
[INFO] [2019-10-13 06:03:31] Storing 5133 ScientificNames
[INFO] [2019-10-13 06:03:31] Processing group of 5133 in 6 groups of 1000
[INFO] [2019-10-13 06:03:33] Average Time: 0.335
[INFO] [2019-10-13 06:03:33] Total Time: 3s
[INFO] [2019-10-13 06:03:33] Storing 5133 Nodes
[INFO] [2019-10-13 06:03:33] Processing group of 5133 in 6 groups of 1000
[INFO] [2019-10-13 06:03:35] Average Time: 0.303
[INFO] [2019-10-13 06:03:35] Total Time: 2s
[INFO] [2019-10-13 06:03:35] Storing 2892 Occurrences
[INFO] [2019-10-13 06:03:35] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-13 06:03:35] Average Time: 0.103
[INFO] [2019-10-13 06:03:35] Total Time: 1s
[INFO] [2019-10-13 06:03:35] Storing 5780 TraitsReferences
[INFO] [2019-10-13 06:03:35] Processing group of 5780 in 6 groups of 1000
[INFO] [2019-10-13 06:03:36] Average Time: 0.085
[INFO] [2019-10-13 06:03:36] Total Time: 1s
[INFO] [2019-10-13 06:03:36] Storing 5779 Traits
[INFO] [2019-10-13 06:03:36] Processing group of 5779 in 6 groups of 1000
[INFO] [2019-10-13 06:03:38] Average Time: 0.312
[INFO] [2019-10-13 06:03:38] Total Time: 2s
[INFO] [2019-10-13 06:03:38] Storing 5778 MetaTraits
[INFO] [2019-10-13 06:03:38] Processing group of 5778 in 6 groups of 1000
[INFO] [2019-10-13 06:03:39] Average Time: 0.12
[INFO] [2019-10-13 06:03:39] Total Time: 1s
[STOP] [2019-10-13 06:03:39] parse_diff_and_store
[START] [2019-10-13 06:03:39] resolve_keys
[INFO] [2019-10-13 06:04:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 06:04:03] traits to occurrences...
[INFO] [2019-10-13 06:04:04] traits to nodes (through occurrences)...
[INFO] [2019-10-13 06:04:04] Traits to sex term...
[INFO] [2019-10-13 06:04:05] Traits to lifestage term...
[INFO] [2019-10-13 06:04:07] MetaTraits to traits...
[INFO] [2019-10-13 06:04:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 06:04:08] Assocs to occurrences...
[INFO] [2019-10-13 06:04:08] Assocs to nodes...
[INFO] [2019-10-13 06:04:08] Assoc to sex term...
[INFO] [2019-10-13 06:04:08] Assoc to lifestage term...
[STOP] [2019-10-13 06:04:08] resolve_keys
[START] [2019-10-13 06:04:08] hold_for_later_1
[STOP] [2019-10-13 06:04:08] hold_for_later_1
[START] [2019-10-13 06:04:08] hold_for_later_2
[STOP] [2019-10-13 06:04:08] hold_for_later_2
[START] [2019-10-13 06:04:08] resolve_missing_parents
[STOP] [2019-10-13 06:04:18] resolve_missing_parents
[START] [2019-10-13 06:04:18] rebuild_nodes
[START] [2019-10-13 06:04:18] Flattener#flatten
[START] [2019-10-13 06:04:18] Flattener#study_resource
[START] [2019-10-13 06:04:18] Flattener#build_ancestry
[STOP] [2019-10-13 06:04:18] Flattener#build_ancestry
[INFO] [2019-10-13 06:04:18] 5133 ancestry keys
[START] [2019-10-13 06:04:18] build_node_ancestors
[INFO] [2019-10-13 06:04:18] old ancestors deleted.
[STOP] [2019-10-13 06:04:19] build_node_ancestors
[START] [2019-10-13 06:04:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 06:04:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 06:04:20] Flattener#flatten
[STOP] [2019-10-13 06:04:20] rebuild_nodes
[START] [2019-10-13 06:04:20] resolve_missing_media_owners
[STOP] [2019-10-13 06:04:20] resolve_missing_media_owners
[START] [2019-10-13 06:04:20] sanitize_media_verbatims
[STOP] [2019-10-13 06:04:20] sanitize_media_verbatims
[START] [2019-10-13 06:04:20] queue_downloads
[STOP] [2019-10-13 06:04:20] queue_downloads
[START] [2019-10-13 06:04:20] parse_names
[WARN] [2019-10-13 06:04:20] I see 5133 names which still need to be parsed.
[STOP] [2019-10-13 06:04:25] parse_names
[START] [2019-10-13 06:04:25] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 06:04:25] denormalize_canonical_names_to_nodes
[START] [2019-10-13 06:04:25] match_nodes
[START] [2019-10-13 06:04:25] map_all_nodes_to_pages
[STOP] [2019-10-13 06:09:33] map_all_nodes_to_pages
[INFO] [2019-10-13 06:09:33] 268 Unmatched nodes (of 5133)! That's too many to output. First 10: Orthriophis taeniura (#49946639); Limnodromus (#49943748); Philomachus pugnax (#49944224); Egretta intermedia (#49941791); Streptopelia dusumieri (#49941611); Coturnix chinensis (#49942358); Charybdis erythrodactyla (#49946120); Gonioinfradens paucidentata (#49946635); Neoliomera richtersoides (#49944130); Dardanus scutellatus (#49943430)
[START] [2019-10-13 06:09:33] update_nodes
[STOP] [2019-10-13 06:09:35] update_nodes
[STOP] [2019-10-13 06:09:35] match_nodes
[START] [2019-10-13 06:09:35] reindex_search
[STOP] [2019-10-13 06:09:48] reindex_search
[START] [2019-10-13 06:09:48] normalize_units
[STOP] [2019-10-13 06:09:48] normalize_units
[START] [2019-10-13 06:09:48] calculate_statistics
[STOP] [2019-10-13 06:09:48] calculate_statistics
[START] [2019-10-13 06:09:48] complete_harvest_instance
[START] [2019-10-13 06:09:48] overall_tsv_creation
[INFO] [2019-10-13 06:09:48] Processing group of 5133 in 1 batches of 10000
[INFO] [2019-10-13 06:10:56] 2890 Traits (unfiltered)...
[INFO] [2019-10-13 06:11:10] 2890 Traits (filtered)...
[INFO] [2019-10-13 06:11:10] 0 Associations (filtered)...
[INFO] [2019-10-13 06:11:52] 14447 metadata added.
[INFO] [2019-10-13 06:11:52] 0 metadata added.
[INFO] [2019-10-13 06:11:52] Average Time: 99.84
[INFO] [2019-10-13 06:11:52] Total Time: 2m4s
[STOP] [2019-10-13 06:11:52] overall_tsv_creation
[INFO] [2019-10-13 06:11:52] Done. Check your files:
[INFO] [2019-10-13 06:11:52] (5133 lines) /app/public/data/guam_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 06:11:52] (11373 lines) /app/public/data/guam_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 06:11:52] (5133 lines) /app/public/data/guam_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 06:11:53] (2891 lines) /app/public/data/guam_sp_list/publish_traits.tsv
[INFO] [2019-10-13 06:11:53] (14448 lines) /app/public/data/guam_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 06:11:53] complete_harvest_instance
[START] [2019-10-13 06:11:53] completed
[STOP] [2019-10-13 06:11:53] completed
[STOP] [2019-10-13 06:11:53] logged process, took 523.66
Latest Process

13 Oct 06:03 EXITED currently processing 0